Mercurial > repos > peterjc > seq_select_by_id
comparison tools/seq_select_by_id/seq_select_by_id.xml @ 6:91f55ee8fea5 draft
v0.0.11; more tests and assorting minor changes
author | peterjc |
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date | Wed, 13 May 2015 10:56:29 -0400 |
parents | 6842c0c7bc70 |
children | a5602454b0ad |
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5:1a83f5ab9e95 | 6:91f55ee8fea5 |
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1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6"> | 1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.11"> |
2 <description>from a tabular file</description> | 2 <description>from a tabular file</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.62">biopython</requirement> | 4 <requirement type="package" version="1.62">biopython</requirement> |
5 <requirement type="python-module">Bio</requirement> | 5 <requirement type="python-module">Bio</requirement> |
6 </requirements> | 6 </requirements> |
7 <version_command interpreter="python">seq_select_by_id.py --version</version_command> | |
8 <command interpreter="python"> | |
9 seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file | |
10 </command> | |
11 <stdio> | 7 <stdio> |
12 <!-- Anything other than zero is an error --> | 8 <!-- Anything other than zero is an error --> |
13 <exit_code range="1:" /> | 9 <exit_code range="1:" /> |
14 <exit_code range=":-1" /> | 10 <exit_code range=":-1" /> |
15 </stdio> | 11 </stdio> |
12 <version_command interpreter="python">seq_select_by_id.py --version</version_command> | |
13 <command interpreter="python"> | |
14 seq_select_by_id.py "$input_tabular" "$column" "$input_file" "$input_file.ext" "$output_file" | |
15 </command> | |
16 <inputs> | 16 <inputs> |
17 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> | 17 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file to select from" help="FASTA, QUAL, FASTQ, or SFF format." /> |
18 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> | 18 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
19 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> | 19 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> |
20 </inputs> | 20 </inputs> |
21 <outputs> | 21 <outputs> |
22 <data name="output_file" format="fasta" label="Selected sequences"> | 22 <data name="output_file" format_source="input_file" metadata_source="input_file" label="Selected sequences from $input_file.name"/> |
23 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
24 <change_format> | |
25 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
26 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
27 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
28 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
29 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
30 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
31 </change_format> | |
32 </data> | |
33 </outputs> | 23 </outputs> |
34 <tests> | 24 <tests> |
35 <test> | 25 <test> |
36 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> | 26 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> |
37 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> | 27 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> |
38 <param name="column" value="1" /> | 28 <param name="column" value="1" /> |
39 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> | 29 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> |
30 <assert_stdout> | |
31 <has_line line="Indexed 10 sequences" /> | |
32 <has_line line="Selected 1 sequences by ID" /> | |
33 </assert_stdout> | |
34 </test> | |
35 <!-- this version has white space in the identifier column (id and description) --> | |
36 <test> | |
37 <param name="input_file" value="k12_ten_proteins.fasta" ftype="fasta" /> | |
38 <param name="input_tabular" value="k12_hypothetical_alt.tabular" ftype="tabular" /> | |
39 <param name="column" value="1" /> | |
40 <output name="output_file" file="k12_hypothetical.fasta" ftype="fasta" /> | |
41 <assert_stdout> | |
42 <has_line line="Indexed 10 sequences" /> | |
43 <has_line line="Selected 1 sequences by ID" /> | |
44 </assert_stdout> | |
45 <assert_stderr> | |
46 <has_line line="WARNING: Some of your identifiers had white space in them, using first word only. e.g.:" /> | |
47 </assert_stderr> | |
48 </test> | |
49 <test expect_failure="true" expect_exit_code="1"> | |
50 <param name="input_file" value="empty.fasta" ftype="fasta" /> | |
51 <param name="input_tabular" value="k12_hypothetical.tabular" ftype="tabular" /> | |
52 <param name="column" value="1" /> | |
53 <assert_stdout> | |
54 <has_line line="Indexed 0 sequences" /> | |
55 </assert_stdout> | |
56 <assert_stderr> | |
57 <has_line line="Identifier 'gi|16127999|ref|NP_414546.1|' not found in sequence file" /> | |
58 </assert_stderr> | |
40 </test> | 59 </test> |
41 </tests> | 60 </tests> |
42 <help> | 61 <help> |
43 **What it does** | 62 **What it does** |
44 | 63 |
67 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | 86 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
68 | 87 |
69 This tool is available to install into other Galaxy Instances via the Galaxy | 88 This tool is available to install into other Galaxy Instances via the Galaxy |
70 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id | 89 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id |
71 </help> | 90 </help> |
91 <citations> | |
92 <citation type="doi">10.7717/peerj.167</citation> | |
93 <citation type="doi">10.1093/bioinformatics/btp163</citation> | |
94 </citations> | |
72 </tool> | 95 </tool> |